Working figs for BATI Report

# set up =======================================================================

library(here)
library(readr)
library(dplyr)
library(ggplot2)
library(sf)

options(readr.show_col_types = FALSE)
options(dplyr.warnings = FALSE)

# read in the functions files
source(here::here("./R/00_global_funs.R"))
source(here::here("./R/01_plots_functions.R"))

fish_data <- readr::read_csv(
    here::here("./data/bati_fish_data_2023-10-04.csv")
) %>%
    standardize_names()
seaway_data <- readr::read_csv(
    here::here("./data/bati_seaway_distances_to_farms.csv")
)

## New names:
## • `` -> `...1`

site_data <- readr::read_csv(here::here("./data/bati_site_data_2023-10-04.csv"))
farm_activity <- readxl::read_xlsx(here::here("./data/farm_activity.xlsx"))
geo_data <- sf::read_sf(here::here("./data/geo-spatial/shapefile/"))
farm_locs <- readr::read_csv(
    here::here("./data/geo-spatial/farm-locations.csv")
)
sampling_locs <- readr::read_csv(
    here::here("./data/geo-spatial/bati_site_master_list.csv")
)
head_dists <- readr::read_csv(
    here::here("./data/headwater-distances.csv")
)
inventory <- readr::read_csv(
    here::here("./data/old-farm-data.csv")
) %>% dplyr::mutate(
    date = lubridate::ym(
        paste(year, month, sep = "-")
    )
)

# some data cleaning ===========================================================
fish_data <- lice_data_clean(fish_data, sampling_locs)

inventory <- inventory[which(inventory$month %in% c(3:6)), ]

# put some initial plots =======================================================
plot_study_area(
    geo_data, farm_locs, sampling_locs,
    to_save = TRUE
)

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## all geometries

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time_series_lice(
    fish_data, sampling_locs, inventory
)

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maps_with_data(
    inventory, fish_data, sampling_locs, farm_locs, geo_data
)

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headwater_distances(
    head_dists, fish_data
)

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